Several classes of viruses form stable associations with their hosts by the integration of one or more copies of the viral genome into host cell DNA. Retroviruses provide a unique and important system for the study of this process since exogenously acquired genomes are integrated at a specific site in the viral genome, but at a large number of sites in cellular DNA. Molecular clones of several newly integrated retroviral genomes were produced in either plasmid or bacteriophage cloning vehicles using approved recombinant DNA techniques and were characterized using electron microscope heteroduplex and R-looping methods. The major objective of these studies has been the application of physical and biochemical techniques to assess the influence of flanking cellular sequences on subsequent viral function and to define in molecular terms those events which take place during integrative recombination.